Variant report

Variant	rs13425734
Chromosome Location	chr2:182677561-182677562
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:182677199..182679031-chr2:182756675..182758841,2	MCF-7	breast:
2	chr2:182675680..182677290-chr2:182677371..182678893,2	MCF-7	breast:
3	chr2:182633341..182635444-chr2:182677151..182679786,2	MCF-7	breast:
4	chr2:182671198..182673524-chr2:182676933..182678703,2	K562	blood:
5	chr2:182677255..182678837-chr2:182768538..182770841,2	K562	blood:
6	chr2:182676782..182679506-chr2:182680066..182682576,2	K562	blood:

Variant related genes	Relation type
ENSG00000138434	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10165226	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10165936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10173114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10176061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10176613	1.00[CEU][hapmap]
rs10176757	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs10179363	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10179547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182213	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10183527	0.82[AFR][1000 genomes]
rs10190772	0.87[YRI][hapmap]
rs10199645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10200243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10201303	1.00[CEU][hapmap]
rs10210215	1.00[CEU][hapmap]
rs10221891	1.00[CEU][hapmap]
rs1106013	0.96[ASN][1000 genomes]
rs11884097	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs11886921	0.88[AFR][1000 genomes]
rs11895376	0.87[YRI][hapmap]
rs11901603	0.88[AFR][1000 genomes]
rs11902910	0.91[AFR][1000 genomes]
rs12620859	0.82[EUR][1000 genomes]
rs13404156	1.00[CEU][hapmap]
rs13414894	0.88[AFR][1000 genomes]
rs13415272	0.89[AFR][1000 genomes]
rs13424337	0.89[AFR][1000 genomes]
rs13428496	0.90[AFR][1000 genomes]
rs1343793	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1528024	1.00[CEU][hapmap]
rs1528025	1.00[CEU][hapmap]
rs1528027	1.00[CEU][hapmap]
rs16867498	1.00[CEU][hapmap]
rs16867500	0.82[JPT][hapmap]
rs16867509	1.00[CEU][hapmap]
rs1881158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1881159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2037799	0.83[AFR][1000 genomes]
rs2059702	1.00[CEU][hapmap]
rs2288330	1.00[CEU][hapmap]
rs2303554	1.00[CEU][hapmap]
rs2368224	1.00[CEU][hapmap]
rs2368225	0.84[AFR][1000 genomes]
rs3731693	1.00[CEU][hapmap]
rs3815877	1.00[CEU][hapmap]
rs3815878	1.00[CEU][hapmap]
rs6433943	1.00[CEU][hapmap]
rs6707164	1.00[CEU][hapmap]
rs6720109	1.00[CEU][hapmap]
rs6720702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6730859	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6735322	1.00[CEU][hapmap]
rs6736766	1.00[CEU][hapmap]
rs6748354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6751685	1.00[CEU][hapmap]
rs6754192	1.00[CEU][hapmap]
rs6754481	0.82[AFR][1000 genomes]
rs6755017	1.00[CEU][hapmap]
rs7557969	1.00[CEU][hapmap]
rs7562680	1.00[CEU][hapmap]
rs7567220	0.88[AFR][1000 genomes]
rs7580410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7603721	1.00[CEU][hapmap]
rs7608942	1.00[CEU][hapmap]
rs9288073	0.88[AFR][1000 genomes]
rs9288074	0.87[AFR][1000 genomes]
rs937297	0.96[ASN][1000 genomes]
rs950165	0.96[ASN][1000 genomes]
rs951542	0.87[AFR][1000 genomes]
rs951543	0.88[AFR][1000 genomes]
rs9807949	1.00[CEU][hapmap]
rs9808112	1.00[CEU][hapmap]
rs9808113	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1001558	chr2:182590009-182732738	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv834478	chr2:182654811-182843201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13425734	LOC647288///LOC730587	trans	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182671000-182678400	Weak transcription	Aorta	Aorta
2	chr2:182671200-182678800	Weak transcription	NHLF	lung
3	chr2:182671200-182682600	Weak transcription	Fetal Stomach	stomach
4	chr2:182674200-182678800	Weak transcription	Small Intestine	intestine
5	chr2:182675200-182678000	Enhancers	NHEK	skin
6	chr2:182675200-182680200	Enhancers	Dnd41	blood
7	chr2:182675400-182677600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:182675400-182679000	Enhancers	HMEC	breast
9	chr2:182675400-182679200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr2:182675400-182679200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:182675400-182680000	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr2:182675800-182677800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:182675800-182678000	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr2:182676000-182678600	Weak transcription	Fetal Lung	lung
15	chr2:182676000-182678800	Weak transcription	NHDF-Ad	bronchial
16	chr2:182676000-182680400	Enhancers	Fetal Thymus	thymus
17	chr2:182676200-182677600	Enhancers	Muscle Satellite Cultured Cells	--
18	chr2:182676200-182678800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:182676200-182680200	Enhancers	Hela-S3	cervix
20	chr2:182676200-182682600	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:182676400-182678000	Weak transcription	K562	blood
22	chr2:182676400-182678600	Weak transcription	HepG2	liver
23	chr2:182676400-182678600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr2:182676400-182679400	Enhancers	HUVEC	blood vessel
25	chr2:182676800-182677800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:182676800-182677800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:182676800-182677800	Weak transcription	Placenta	Placenta
28	chr2:182676800-182679200	Enhancers	Thymus	Thymus
29	chr2:182676800-182679600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:182676800-182679600	Weak transcription	Stomach Mucosa	stomach
31	chr2:182676800-182680200	Enhancers	Placenta Amnion	Placenta Amnion
32	chr2:182676800-182681200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:182676800-182682400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:182676800-182686400	Weak transcription	Pancreas	Pancrea
35	chr2:182677000-182678600	Weak transcription	HSMM	muscle
36	chr2:182677200-182678200	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr2:182677200-182678600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:182677200-182678600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:182677200-182678800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:182677200-182683600	Weak transcription	Fetal Kidney	kidney
41	chr2:182677400-182678000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr2:182677400-182678600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr2:182677400-182678600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:182677400-182678600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr2:182677400-182678600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:182677400-182678600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:182677400-182678600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:182677400-182678600	Weak transcription	NH-A	brain
49	chr2:182677400-182678800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:182677400-182678800	Weak transcription	HSMMtube	muscle

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